So, what tool does that invoke to do the ISP? [I'm not an expert Studio7 user] Is there a detailed log of the commands that do the ISP? Can you make it as "verbose" as practical for this exercise?

Does the command to do the ISP call out doing EEPROM as well as flash? Is the .EEP file created, or perhaps part of .ELF? What file does the log show is being opened and transmitted to do the EEPROM programming? What are the verification results?

You can put lipstick on a pig, but it is still a pig.

I've never met a pig I didn't like, as long as you have some salt and pepper.

Second vote for EESAVE. Depending on the order you program things it could be that the data you put into the EEPROM is simply erased by the next programming of the Flash as "Chip Erase" erases both Flash and EEPROM unless EESAVE is activated.